lncRNA Structure Prediction

I. Result for minimum free energy prediction

The optimal secondary structure in dot-bracket notation with a minimum free energy of (-532.40) is given below.

1. Sequence-
AAAAAAAAAAAAAAUGAUUAAGGAUUAGCGAUCUAAUAGAUCAGGAAAAUUCAAAUUCAA
AUUCAAAUUCAAAUGUUUUGAAAAGGAAAAAUGUCUACUAACAAAACAUAGUCAAAUAAG
AAGAUCAGCUAAAGAAACAAGUUCAAAUAGCAGAAUAGUUUUAGACUAUUUGAGGCGAGA
UUGGAAAGUUCUAAAACAUGAAAGAGAGGGAAAUGCUCUUUUCAAGACUUAACUACCAAC
AUGCUUGGAAAACAAAUCAUAGAAAAAACUCACCCCAAUAGGCCAAAGAUUUGAUUUUAA
ACAUGGAAACUAGAUGGCUAAAACAAGUAGGUCUUAACCAGGUUAUUAUCAUUCAAUUGA
ACUUGUAAAGGGUUUUGCUAGCACACGAGAAACUUAACUAAAUCGUGCUAACAGAUGAUA
GACAAGAUUGCCCACUAAGUCUAUUCAAGGCAAGCAAUUCUAGUUAAUACCACCUGAACA
UACCACCUUAAUUAUCUGAAAACACCUCACAGGGUGAUUUCUACCACACAUCCAUCCAAA
CCAAGUGACACUAGCAGAUUUGAGAGGGUGAAUCUAGAAACAAGCGAUUGCUAUGACCCC
AUUUGCGUACCUAACUAGUUAGCUCAUAAUAAUCCUGGAGUUGACCCUCGUUUUAGGUUU
UCAAGCACAAAUAGGUCACCAAAAAGAGACAUGCUUCAGCAUAUUAAUAGUAAUCAACUG
UAAGAUCUGAUGACAGUUUUGAGACAUCAAACCAUCUCUUAUAUUUUCUCGUUCCUGAAU
UUGUGGACCUGGCCAUGUGAUAAUAAAGAGCAAUGGAAUGCAAUGGAAUCAUAGCUUGAA
CUAGCAAUGGAGAUUUAAAACAAUGACUUAAUCAGACACAAAGUUGAUCACAAUAGCACU
GAAACAUGUUAAACCCAGAACACUGCUGACACCUAAAUUUAAAUCAAUAAUUUGUACGGG
GAAGAAACCAAACCCACAAGCUGGAACACACAGCAAACAUGAUUACUCAAAUGACAUGUA
ACAUUCCUCAGGCCAACAGAUCCUUUCCUAUAGGCUUUCACUUUAACAUACAAAGGAAGG
UUAUUUAAUCAAGAUAUGAAAUAUGUUGCUAACACUGAUCUUGAACCUAGAUGUCUAUUC
CCUAAGCAUGCAUGACUAUGUCUUUCAAAGCAACAAUAUGGAUAAUCAACCUCACAUAAC
UAAUCUCCAGACAAACAAGAGUGAGCAUUCCUAGGAACUCACAGAAACAGAGAAAAUUCA
CAACAUGCUGAUAUCUCAGGUUCAAUAGACUCAACAAACAGACACGAAUCCAACUUGAUU
UACCUAAAAUAUACAUAUUCAUGACCACAGAUAGAAUAUAGUAGCAAUUAUAAUGGAGCA
GUGGACUUUCAAGAAUAACGGCAUGGUAUGGAGGACCCUUGUCUCAUCUCCUAGCCUCAG
ACUGUCGGGGGACCUUCAUUAAAGCCUUCAGACUCACAUCCAAGGCUCAGCACUUCUCAA
AUGAUACAACAUUCAGGCAGAUUAAAACAUUCGGGAGUCUAAAAACAGCAACCACAGGCU
CAAAAAAAACUACAAGAGAACAGAGGGCUAACAUUGAAGAGAAAUACUUAACUACAACCA
AAUUGCUGAAGGCUAACCUCAAAUACUAUGCAUUCAAGUGAGAUCCUUAAGAUCAAAUAU
CCUAUGAAUCUGAUAGUACUAACAGCAAAUGUGGCUUACCCAAGAUCGAAAUACACUCUU
UGCCAUAGAUCUAAGACCAAAUGGUACAGAACCAGACGCAAGUAUUUACCAAUCAUACAA
UUUAACUCACAUAAACUGGUCACAUGUCCCUCAUGGACACUGUUAGUGCUGAAGAUGAGA
AAUUAGUAUCUAACAUGCUACAGUUCACAGAUAUGGAAAAUUUCACAUAAAACGUGUAAC
UUUAUUUAAAAUAGGAACCAAAGUAGUCAUACUCUCAAACAUGAUACUGGAUCAAACAUG
UAAGGGAGAAAUCAUGCAAGUCGUCCAAGAUAACGCCAUAGACACAUUUGACCUAGACAU
AGAAUAGACUAAGGCUCCAACUUUAGAAAUAAUAUUAUUGCAGUCAAAAUUUAAAGCAUA
UCUAUCUUUUCUUCUUAUACACCCAAAUCAACACAAAAACUUUUCAAGACAGUAAAGGAA
CUUCAGCAAAACAAGUAGAAAACAACCUAAUCUUCUCAGGAAAAAUUUAAAUCUCAUUAA
UAGAUCAUCAAACAAACUAAAUCAGAGAAUUUUACUUUCUAUUAGUUCUAACAUUGAACC
AAAACUUCAUGACAAACACGAAUACCUAUUUAUAAACAAGAAAACAAAAAAACAGAGUCA
UACUAAGUCAUAAAAAUUAGAGUGCUAAGUCCAUUUUAACCUGGGUAAGUUUAUUUAUCA
AACUACUGAUCUGAACACCACACGAAUAGGUUAUUACUCAUACUAAAAAGGUAGAAUAUA
CACUGAAAACCAGCUAUUUAACUGAAAUAUCAAGAAAAUGAGACAGAAUUUAGGGUUUUA
CCUAGUUUGGGCAGGAAGCUAGGAUGUUAAUAGGUUGAAGUGAUUCUUCGCUACCUUGAG
CCUUGAUUUCAGCUCUUUUAAGCUUCUACUACGUUCAUAAACCGACAGUGGAAAUGAGGC
UCACAUUUGCACUAAACUCGAGGGAAAGCGAUUCCAACAAUGCCAUGGCUGCAAAAACUA
CAAAGUUGGAGUAUGCCCCGCCAAGAUACGAGUCGGAUAACCUUAAACGCCUGAGUACUC
AUCUCAGAAGAGAAUAACUAUUGACAGCAUGAUCAUCACCUCUUUCAAUCCCUCGAUUAG
GCCCACCCCCACAGUAUCCAACACACCAUACUUGUAGACGUCAGAAAAUCAGAGUG

2. MFE structure-
..............(((((..(((((...(((((...))))).....)))))...(((...((((((.........))))))...)))..((((((((.........((((((...(((((...((.((((..(((.....)))...)))).))....)))))))))))((((((((((((.(((..(((((......((
((.(((((.......)))))))))....(((((((......((((((........................((((....(((((....(((((.(((((..(((.........)))..)))))))))).)))))....(((((.....(((......))))))))....))))((((.((((((................
....)))))).)))).(((((((.((........))..))))))).....))))))....)))))))...........(((((((((..........((((.(((((....))))).))))..((((...(((((.......((((((........((((((((.(((((............(((....))).(((((..
(((((.((((((((...((((((((............)))))))).......))))))......)).))))).))))).........((((((.(((((..((((....((.(((((((......((((((...((((((((....)))).(((((((((.((((.((.((((((.........))).......))).))
.)))))))))..)))).............(((.(((......))).)))...............))))..)))))).....))))))).))))))...))))).)))))).....(((.......))).)))))...))))))))......((((..(((............)))))))((((.......))))..((((
(.(((......))))))))..........(((((...((........))...)))))))))))..............((((.....(((((((....((....((((........((((((((((((((((((((.........((((((..(((.....(((((.............((((..................
.....))))...........(((((..(((....))))))))......)))))....)))...))))))))))))).)))))))..))).))).......))))....))...))))))).))))......(((((((((((........)).)))))).))).........)))))...))))...............)
)..))))))).))))).....))).)))))...)))))))(((((.(((((..(((((....(((((((...(((.......((((((......(((....(((........)))...))).............))))))......(((........)))...............)))....))))))).....))))).
...........((((.......(((((((((..............(((((...(((((((.((((.....)))).....((((((..((((..((((((((((((....((((((..........................)))))).......(((((..((((.....)))).......((((.........))))..
................)))))...(((((.....))))))))))))))))).)))).......((((((.....)))))).(((((((...(((((((...))).))))....))).)))).........))))))......(((......(((((..(((((.............)))))..)))))......)))..(
((..................))).)))))))......)))))......((((((......))))))............(((..............)))......((((((((((((.............................)))).)).)))))).))))))))).....))))(((((..(((((((((((((..
...........((.....(((((.(((.......((((((...(((((.......))))).)))))).......)))........(((.((.....)).))).((((((((....................((..((.(((.((((..........)))).)))))..))(((........)))....(((((...((((
......)))).))))).......))))))))......((.((((.....)))))).......(((.....)))))))).....)).............))))).)))..)))))))))).((((((((.......))))))))........((((...(((((....)))))))))((((((((......((((......
))))((((((..(((........)))))))))...)))))))).....((.((((..((((((((...((((((.......((...((((((...((((....))))...))).)))..))........))))))...............(((((.......)))))(((((...........................)
))))....))))))))))))))...))))))))))..................)))))))).....))))).....

You can download the minimum free energy (MFE) structure in Vienna Format

II. Results for thermodynamic ensemble prediction

1. The free energy of the thermodynamic ensemble is [-583.19] kcal/mol.

2. The frequency of mfe structure in ensemble 1.62452e-36.

3. The ensemble diversity 679.78.

4. You may look at the dot plot containing the base pair probabilities [below]

Download Dot plot JPG EPS

III. Graphical output

1. A note on base-pairing probabilities:--

The structure below is colored by base-pairing probabilities. For unpaired regions the color denotes the probability of being unpaired. The reliability information of RNA secondary structure plot in the form of color annotation, Positional entropy ranging from red (low entropy, well-defined) via green to blue and violet (high entropy, ill-defined).

Download RNA structure JPG EPS

2. Here you find a mountain plot representation of the MFE structure, the thermodynamic ensemble of RNA structures, and the centroid structure. Additionally we present the positional entropy for each position. The resulting plot shows three curves, two mountain plots derived from the MFE structure (red) and the pairing probabilities (black) and a positional entropy curve (green). Well-defined regions are identified by low entropy.

Download mountain plot JPG EPS